SMTL ID : 6gmc.1

1.2 A resolution structure of human hydroxyacid oxidase 1 bound with FMN and 4-carboxy-5-[(4-chlorophenyl)sulfanyl]-1,2,3-thiadiazole

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.20 Å

Oligo State

homo-tetramer

Ligands

16 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.1: 9 residues within 4Å: Chain A: V.159, P.162 Chain C: R.52, M.53, L.54, R.55, A.345, L.346, G.348 Ligand excluded by PLIP EDO.2: 4 residues within 4Å: Chain A: G.284, K.285, V.286, E.287 Ligand excluded by PLIP EDO.3: 4 residues within 4Å: Chain A: R.28, L.37, A.38, I.41 Ligand excluded by PLIP EDO.4: 6 residues within 4Å: Chain A: C.7, K.296, E.339 Chain D: N.32, D.33, L.168 Ligand excluded by PLIP EDO.7: 9 residues within 4Å: Chain B: V.159, P.162 Chain D: R.52, M.53, L.54, R.55, A.345, L.346, G.348 Ligand excluded by PLIP EDO.8: 4 residues within 4Å: Chain B: G.284, K.285, V.286, E.287 Ligand excluded by PLIP EDO.9: 4 residues within 4Å: Chain B: R.28, L.37, A.38, I.41 Ligand excluded by PLIP EDO.10: 6 residues within 4Å: Chain B: C.7, K.296, E.339 Chain C: N.32, D.33, L.168 Ligand excluded by PLIP EDO.13: 9 residues within 4Å: Chain B: R.52, M.53, L.54, R.55, A.345, L.346, G.348 Chain C: V.159, P.162 Ligand excluded by PLIP EDO.14: 4 residues within 4Å: Chain C: G.284, K.285, V.286, E.287 Ligand excluded by PLIP EDO.15: 4 residues within 4Å: Chain C: R.28, L.37, A.38, I.41 Ligand excluded by PLIP EDO.16: 6 residues within 4Å: Chain A: N.32, D.33, L.168 Chain C: C.7, K.296, E.339 Ligand excluded by PLIP EDO.19: 9 residues within 4Å: Chain A: R.52, M.53, L.54, R.55, A.345, L.346, G.348 Chain D: V.159, P.162 Ligand excluded by PLIP EDO.20: 4 residues within 4Å: Chain D: G.284, K.285, V.286, E.287 Ligand excluded by PLIP EDO.21: 4 residues within 4Å: Chain D: R.28, L.37, A.38, I.41 Ligand excluded by PLIP EDO.22: 6 residues within 4Å: Chain B: N.32, D.33, L.168 Chain D: C.7, K.296, E.339 Ligand excluded by PLIP

4 x FMN: FLAVIN MONONUCLEOTIDE(Non-covalent)

FMN.5: 22 residues within 4Å: Chain A: Y.26, Y.27, A.79, T.80, A.81, S.108, Q.130, Y.132, T.158, K.236, S.258, H.260, G.261, R.263, D.291, G.292, G.293, R.295, V.313, G.314, R.315 Ligands: C7C.6 27 PLIP interactions: 27 interactions with chain A Hydrophobic interactions: A:Y.26, A:Y.27, A:T.80, A:R.315 Hydrogen bonds: A:A.79, A:A.79, A:A.81, A:S.108, A:Q.130, A:Q.130, A:K.236, A:K.236, A:S.258, A:G.261, A:G.292, A:G.293, A:G.314, A:R.315 Water bridges: A:H.260, A:D.291, A:D.291, A:V.294, A:V.294, A:R.295, A:R.315 Salt bridges: A:R.295, A:R.315 FMN.11: 22 residues within 4Å: Chain B: Y.26, Y.27, A.79, T.80, A.81, S.108, Q.130, Y.132, T.158, K.236, S.258, H.260, G.261, R.263, D.291, G.292, G.293, R.295, V.313, G.314, R.315 Ligands: C7C.12 27 PLIP interactions: 27 interactions with chain B Hydrophobic interactions: B:Y.26, B:Y.27, B:T.80, B:R.315 Hydrogen bonds: B:A.79, B:A.79, B:A.81, B:S.108, B:Q.130, B:Q.130, B:K.236, B:K.236, B:S.258, B:G.261, B:G.292, B:G.293, B:G.314, B:R.315 Water bridges: B:H.260, B:D.291, B:D.291, B:V.294, B:V.294, B:R.295, B:R.315 Salt bridges: B:R.295, B:R.315 FMN.17: 22 residues within 4Å: Chain C: Y.26, Y.27, A.79, T.80, A.81, S.108, Q.130, Y.132, T.158, K.236, S.258, H.260, G.261, R.263, D.291, G.292, G.293, R.295, V.313, G.314, R.315 Ligands: C7C.18 27 PLIP interactions: 27 interactions with chain C Hydrophobic interactions: C:Y.26, C:Y.27, C:T.80, C:R.315 Hydrogen bonds: C:A.79, C:A.79, C:A.81, C:S.108, C:Q.130, C:Q.130, C:K.236, C:K.236, C:S.258, C:G.261, C:G.292, C:G.293, C:G.314, C:R.315 Water bridges: C:H.260, C:D.291, C:D.291, C:V.294, C:V.294, C:R.295, C:R.315 Salt bridges: C:R.295, C:R.315 FMN.23: 22 residues within 4Å: Chain D: Y.26, Y.27, A.79, T.80, A.81, S.108, Q.130, Y.132, T.158, K.236, S.258, H.260, G.261, R.263, D.291, G.292, G.293, R.295, V.313, G.314, R.315 Ligands: C7C.24 27 PLIP interactions: 27 interactions with chain D Hydrophobic interactions: D:Y.26, D:Y.27, D:T.80, D:R.315 Hydrogen bonds: D:A.79, D:A.79, D:A.81, D:S.108, D:Q.130, D:Q.130, D:K.236, D:K.236, D:S.258, D:G.261, D:G.292, D:G.293, D:G.314, D:R.315 Water bridges: D:H.260, D:D.291, D:D.291, D:V.294, D:V.294, D:R.295, D:R.315 Salt bridges: D:R.295, D:R.315

4 x C7C: 5-[(4-chlorophenyl)sulfanyl]-1,2,3-thiadiazole-4-carboxylate(Non-covalent)

C7C.6: 11 residues within 4Å: Chain A: Y.26, M.82, W.110, Y.132, R.167, F.193, L.205, Y.208, H.260, R.263 Ligands: FMN.5 12 PLIP interactions: 12 interactions with chain A Hydrophobic interactions: A:W.110, A:F.193, A:L.205, A:L.205, A:Y.208 Hydrogen bonds: A:Y.26, A:Y.26 Salt bridges: A:R.167, A:H.260, A:R.263 pi-Stacking: A:W.110, A:W.110 C7C.12: 11 residues within 4Å: Chain B: Y.26, M.82, W.110, Y.132, R.167, F.193, L.205, Y.208, H.260, R.263 Ligands: FMN.11 12 PLIP interactions: 12 interactions with chain B Hydrophobic interactions: B:W.110, B:F.193, B:L.205, B:L.205, B:Y.208 Hydrogen bonds: B:Y.26, B:Y.26 Salt bridges: B:R.167, B:H.260, B:R.263 pi-Stacking: B:W.110, B:W.110 C7C.18: 11 residues within 4Å: Chain C: Y.26, M.82, W.110, Y.132, R.167, F.193, L.205, Y.208, H.260, R.263 Ligands: FMN.17 12 PLIP interactions: 12 interactions with chain C Hydrophobic interactions: C:W.110, C:F.193, C:L.205, C:L.205, C:Y.208 Hydrogen bonds: C:Y.26, C:Y.26 Salt bridges: C:R.167, C:H.260, C:R.263 pi-Stacking: C:W.110, C:W.110 C7C.24: 11 residues within 4Å: Chain D: Y.26, M.82, W.110, Y.132, R.167, F.193, L.205, Y.208, H.260, R.263 Ligands: FMN.23 12 PLIP interactions: 12 interactions with chain D Hydrophobic interactions: D:W.110, D:F.193, D:L.205, D:L.205, D:Y.208 Hydrogen bonds: D:Y.26, D:Y.26 Salt bridges: D:R.167, D:H.260, D:R.263 pi-Stacking: D:W.110, D:W.110

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

MacKinnon, S. et al., Structure of human hydroxyacid oxidase 1 bound with FMN and glycolate. To Be Published

Release Date

2018-06-13

Peptides

Hydroxyacid oxidase 1: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
A

D
A

Hydroxyacid oxidase 1

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